Analytical and Bioanalytical Chemistry

, Volume 404, Issue 4, pp 939–965 | Cite as

Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present

Review

Abstract

Mass-spectrometry-based proteomics is continuing to make major contributions to the discovery of fundamental biological processes and, more recently, has also developed into an assay platform capable of measuring hundreds to thousands of proteins in any biological system. The field has progressed at an amazing rate over the past five years in terms of technology as well as the breadth and depth of applications in all areas of the life sciences. Some of the technical approaches that were at an experimental stage back then are considered the gold standard today, and the community is learning to come to grips with the volume and complexity of the data generated. The revolution in DNA/RNA sequencing technology extends the reach of proteomic research to practically any species, and the notion that mass spectrometry has the potential to eventually retire the western blot is no longer in the realm of science fiction. In this review, we focus on the major technical and conceptual developments since 2007 and illustrate these by important recent applications.

Keywords

Quantitative proteomics Liquid chromatography Mass spectrometry Bioinformatics 

Abbreviations

AP

Affinity purification

DDA

Data-dependent acquisition

ESI

Electrospray ionization

HCD

Higher-energy collision-induced dissociation

HDAC

Histone deacetylase

HPLC

High-pressure liquid chromatography

ICP

Inductively coupled plasma

IMAC

Immobilized metal affinity chromatography

iTRAQ

Isobaric tags for absolute and relative quantification

LC

Liquid chromatography

MRM

Multiple reaction monitoring

MS

Mass spectrometry

MS/MS

Tandem mass spectrometry

PAI

Protein abundance index

PrEST

Protein epitope signature tag

PSAQ

Protein standard absolute quantification

PSM

Peptide-to-spectrum match

PTM

Post-translational modification

QTOF

Quadrupole time of flight

SILAC

Stable isotope labeling with amino acids in cell culture

SRM

Selected reaction monitoring

TMT

Tandem mass tag

UPLC

Ultra-high-pressure liquid chromatography

XIC

Extracted ion chromatogram

Notes

Acknowledgments

The authors wish to thank Frank Weissbrodt for help with creating the graphics. We apologize to all authors whose interesting work could not be cited owing to space or conceptual constraints.

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Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  1. 1.Cellzome AGHeidelbergGermany
  2. 2.Chair of Proteomics and BioanalyticsTechnische Universität MünchenFreisingGermany
  3. 3.Center for Integrated Protein Science Munich (CIPSM)MunichGermany

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